[CP2K-user] massive slowdown in SCF timings during MD
Sean Fischer
safisc... at gmail.com
Fri Oct 11 17:28:21 UTC 2019
Hi Matt,
I agree that some of the behavior does look like my resources are being
oversubscribed, but I am sure that I have dedicated access to the nodes I
am using, and I see nothing unusual with top on the nodes I'm using. I have
another test that I ran where I did not get the large fluctuations but
still have the linear trend, though this one was stable for longer before
the increase. See below, and the input file for that run is attached (same
initial geometry but some changes to the other settings).
[image: md_timings2.png]
Best,
Sean
On Friday, October 11, 2019 at 12:10:01 PM UTC-4, Matt W wrote:
>
> Hi Sean,
>
> are you sure you have dedicated access to the resource you run on? Those
> large fluctuations look likely to be caused by other jobs running on the
> node(s) you are using (though the general linearish trend is surprising).
>
> Matt
>
> On Friday, October 11, 2019 at 1:41:03 PM UTC+1, Sean Fischer wrote:
>>
>> I'm attempting to run MD using QS on a 64 molecule water box. So far I
>> have been unable to achieve consistent performance across the MD
>> trajectory. After a while the time per MD step dramatically increases, but
>> the number of SCF iterations per step stays basically constant, as you can
>> see in the included image.
>>
>> [image: md_timing.png]
>>
>> To further illustrate this, the following is from one of the first steps
>> in the trajectory
>>
>>
>> ----------------------------------- OT
>> ---------------------------------------
>>
>> Minimizer : DIIS : direct inversion
>>
>> in the iterative subspace
>>
>> using 7 DIIS vectors
>>
>> safer DIIS on
>>
>> Preconditioner : FULL_ALL : diagonalization, state selective
>>
>> Precond_solver : DEFAULT
>>
>> stepsize : 0.15000000 energy_gap :
>> 0.08000000
>>
>> eps_taylor : 0.10000E-15 max_taylor :
>> 4
>>
>> ----------------------------------- OT
>> ---------------------------------------
>>
>>
>> Step Update method Time Convergence Total energy
>> Change
>>
>>
>> ------------------------------------------------------------------------------
>>
>> 1 OT DIIS 0.15E+00 2.3 0.00030148 -1107.9047914512
>> -1.11E+03
>>
>> 2 OT DIIS 0.15E+00 1.6 0.00012826 -1107.9089080136
>> -4.12E-03
>>
>> 3 OT DIIS 0.15E+00 1.6 0.00007994 -1107.9095257164
>> -6.18E-04
>>
>> 4 OT DIIS 0.15E+00 1.6 0.00000744 -1107.9096948950
>> -1.69E-04
>>
>> 5 OT DIIS 0.15E+00 2.0 0.00000377 -1107.9096964458
>> -1.55E-06
>>
>> 6 OT DIIS 0.15E+00 1.6 0.00000067 -1107.9096967653
>> -3.19E-07
>>
>>
>> *** SCF run converged in 6 steps ***
>>
>>
>>
>> Electronic density on regular grids: -511.9999993695
>> 0.0000006305
>>
>> Core density on regular grids: 511.9999999846
>> -0.0000000154
>>
>> Total charge density on r-space grids: 0.0000006151
>>
>> Total charge density g-space grids: 0.0000006151
>>
>>
>>
>> While after ~2500 steps, the same section now looks like
>>
>>
>> ----------------------------------- OT
>> ---------------------------------------
>>
>> Minimizer : DIIS : direct inversion
>>
>> in the iterative subspace
>>
>> using 7 DIIS vectors
>>
>> safer DIIS on
>>
>> Preconditioner : FULL_ALL : diagonalization, state selective
>>
>> Precond_solver : DEFAULT
>>
>> stepsize : 0.15000000 energy_gap :
>> 0.08000000
>>
>> eps_taylor : 0.10000E-15 max_taylor :
>> 4
>>
>> ----------------------------------- OT
>> ---------------------------------------
>>
>>
>> Step Update method Time Convergence Total energy
>> Change
>>
>>
>> ------------------------------------------------------------------------------
>>
>> 1 OT DIIS 0.15E+00 6.3 0.00003184 -1108.0316770158
>> -1.11E+03
>>
>> 2 OT DIIS 0.15E+00 17.0 0.00001599 -1108.0317180830
>> -4.11E-05
>>
>> 3 OT DIIS 0.15E+00 18.4 0.00000956 -1108.0317247395
>> -6.66E-06
>>
>> 4 OT DIIS 0.15E+00 21.9 0.00000119 -1108.0317273970
>> -2.66E-06
>>
>> 5 OT DIIS 0.15E+00 6.8 0.00000063 -1108.0317274283
>> -3.14E-08
>>
>>
>> *** SCF run converged in 5 steps ***
>>
>>
>>
>> Electronic density on regular grids: -511.9999994472
>> 0.0000005528
>>
>> Core density on regular grids: 511.9999999845
>> -0.0000000155
>>
>> Total charge density on r-space grids: 0.0000005373
>>
>> Total charge density g-space grids: 0.0000005373
>>
>>
>>
>> This has happened with different functionals, pseudopotentials, and SCF
>> parameters (PS vs ASPC extrapolation, different orders of extrapolation, OT
>> DIIS vs DIIS/Diag., different preconditioners). I recompiled the whole code
>> with the toolchain install script generating all dependencies and got the
>> same result. There is no indication from the dynamics of the system itself
>> as to what the problem might be as the potential and kinetic energies are
>> well behaved, and the constant of motion for the dynamics is reasonably
>> conserved. I've watched the resulting trajectory itself, and there is
>> nothing unusually happening (no bonding breaking, etc.) The input file I
>> used for run in the plot above is attached. The starting geometry for the
>> water molecules was taken from the 64 molecule benchmark in the tests/QS
>> directory.
>>
>>
>> If anyone has any suggestions on possible causes or where I can look for
>> more information, I would be very appreciative.
>>
>
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